Addon/Script: Register custom user properties
The filepath properties are stored in bpy.types.UserPreferencesFilePaths, which does not support custom properties (only ID types and Bones do).

Even if it was possible, you couldn't make a property show still - addons can't overrule default layout scripts.

You can use AddonPreferences however, as long as the properties are not supposed to be stored in every individual .blend you work with. AddonPreferences show up in the User Preferences > Addons tab, below the addon info (the addon entry needs to be expanded).